CiteULike: Tag map

A protein interaction map of Drosophila melanogaster.

L Giot — 2005-06-14T01:08:12-00:00

Science, Vol. 302, No. 5651. (5 December 2003), pp. 1727-1736.

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

Continuous Generalization for Small Mobile Displays

Claus And — 2008-01-07T14:21:28-00:00

this paper, this approach is exemplified with a specific simplification operation, namely the simplification of building ground plans

The Mind Map Book

Tony Buzan — 2006-11-24T16:47:19-00:00

(08 May 2003)

Cluster analysis of Wisconsin Breast Cancer dataset using self-organizing maps.

S Pantazi — 2005-11-22T02:49:34-00:00

Stud Health Technol Inform, Vol. 90 (2002), pp. 431-436.

This work deals with multidimensional data analysis, precisely cluster analysis applied to a very well known dataset, the Wisconsin Breast Cancer dataset. After the introduction of the topics of the paper the cluster analysis concept is shortly explained and different methods of cluster analysis are compared. Further, the Kohonen model of self-organizing maps is briefly described together with an example and with explanations of how the cluster analysis can be performed using the maps. After describing the data set and the methodology used for the analysis we present the findings using textual as well as visual descriptions and conclude that the approach is a useful complement for assessing multidimensional data and that this dataset has been overused for automated decision benchmarking purposes, without a thorough analysis of the data it contains.

Stimulus-Specific Adaptations in the Gaze Control System of the Barn Owl

Amit Reches — 2008-02-07T11:45:17-00:00

J. Neurosci., Vol. 28, No. 6. (6 February 2008), pp. 1523-1533.

Abrupt orientation to novel stimuli is a critical, memory-dependent task performed by the brain. In the present study, we examined two gaze control centers of the barn owl: the optic tectum (OT) and the arcopallium gaze fields (AGFs). Responses of neurons to long sequences of dichotic sound bursts comprised of two sounds differing in the probability of appearance were analyzed. We report that auditory neurons in the OT and in the AGFs tend to respond stronger to rarely presented sounds (novel sounds) than to the same sounds when presented frequently. This history-dependent phenomenon, known as stimulus-specific adaptation (SSA), was demonstrated for rare sound frequencies, binaural localization cues [interaural time difference (ITD) and level difference (ILD)] and sound amplitudes. The manifestation of SSA in such a variety of independent acoustic features, in the midbrain and in the forebrain, supports the notion that SSA is involved in sensory memory and novelty detection. To track the origin of SSA, we analyzed responses of neurons in the external nucleus of the inferior colliculus (ICX; the source of auditory input to the OT) to similar sequences of sound bursts. Neurons in the ICX responded stronger to rare sound frequencies, but did not respond differently to rare ITDs, ILDs, or sound amplitudes. We hypothesize that part of the SSA reported here is computed in high-level networks, giving rise to novelty signals that modulate tectal responses in a context-dependent manner. 10.1523/JNEUROSCI.3785-07.2008

Response properties of neighboring neurons in the auditory midbrain for pure-tone stimulation: a tetrode study.

CV Seshagiri — 2007-11-05T16:33:22-00:00

J Neurophysiol, Vol. 98, No. 4. (October 2007), pp. 2058-2073.

The complex anatomical structure of the central nucleus of the inferior colliculus (ICC), the principal auditory nucleus in the midbrain, may provide the basis for functional organization of auditory information. To investigate this organization, we used tetrodes to record from neighboring neurons in the ICC of anesthetized cats and studied the similarity and difference among the responses of these neurons to pure-tone stimuli using widely used physiological characterizations. Consistent with the tonotopic arrangement of neurons in the ICC and reports of a threshold map, we found a high degree of correlation in the best frequencies (BFs) of neighboring neurons, which were mostly <3 kHz in our sample, and the pure-tone thresholds among neighboring neurons. However, width of frequency tuning, shapes of the frequency response areas, and temporal discharge patterns showed little or no correlation among neighboring neurons. Because the BF and threshold are measured at levels near the threshold and the characteristic frequency (CF), neighboring neurons may receive similar primary inputs tuned to their CF; however, at higher levels, additional inputs from other frequency channels may be recruited, introducing greater variability in the responses. There was also no correlation among neighboring neurons' sensitivity to interaural time differences (ITD) measured with binaural beats. However, the characteristic phases (CPs) of neighboring neurons revealed a significant correlation. Because the CP is related to the neural mechanisms generating the ITD sensitivity, this result is consistent with segregation of inputs to the ICC from the lateral and medial superior olives.

Concept mapping and misconceptions: a study of high-school students’ understandings of acids and bases

Bertram Ross — 2008-03-25T08:59:21-00:00

International Journal of Science Education, Vol. 13, No. 1. (1991), pp. 11-23.

This paper reports a study of senior high-school students’ understandings of concepts related to acids and bases. The methodology was grounded on a concept mapconstructed from the curriculum. This map was used in the design of a multiple-choice test and of clinical interviews. It was also used in the analysis of the data, and inconstructing concept maps for each participant. The methodology and the resulting analyses are illustrated with two abbreviated cases selected from the study. It is shown that these participants hold idiosyncratic concepts not consistently coincident with those of the prescribed curriculum, and that everyday concepts are retained more than are scientificconcepts. Discussion of concept mapping points to how it starkly represents gaps in the understanding of concepts that are interrelated. This feature of the methodological approach is shown to be significant to the study of students’ conceptions when the subject-matter concepts are theoretically linked.

Electrophysiological effects of myocardial stretch and mechanical determinants of stretch-activated arrhythmias.

MR Franz — 2006-06-09T08:49:41-00:00

Circulation, Vol. 86, No. 3. (September 1992), pp. 968-978.

BACKGROUND. Although the existence of myocardial mechanoelectrical feedback is well established, the mechanism of arrhythmia induction by ventricular dilatation or stretch remains insufficiently defined. In particular, controversy exists when comparing the arrhythmogenic potential of chronic versus acute myocardial stretch. Also, assessment of cellular electrophysiological effects of myocardial stretch has been incomplete. METHODS AND RESULTS. To evaluate the electrophysiological and arrhythmogenic effects of slow versus rapid ventricular wall stretch, we developed an isolated Langendorff-perfused rabbit heart model in which left ventricular (LV) volume can be changed by a computer-controlled servopump. Cellular electrophysiological effects and premature ventricular excitations (PVEs) and their origin produced by the volume increases were assessed by a multiple-site monophasic action potential (MAP) recording system and by volume-conducted ECGs obtained by immersing the entire preparation in a saline-filled tank. Volume was increased either gradually with slow volume ramps (0.1 ml/sec) or suddenly by volume pulses of varying pulse waveforms (three different amplitudes and five different rise velocities) applied randomly 250-350 times to each of eight hearts. Gradual LV volume loading caused gradual decreases in MAP resting and action potential amplitude, whereas rapid, transient volume pulses caused transient depolarizations. Despite similar membrane potential effects of stretch, gradual volume increases rarely (11%) produced PVEs, even with large volume loads, whereas rapid volume pulses of moderate amplitudes regularly triggered PVEs (45-100% of interventions). Logistic regression analysis showed that the probability of PVE occurrence increased independently with both the amplitude and the velocity of the volume increase, with the greatest sensitivity to stretch velocity exhibited at low and intermediate pulse amplitudes. Faster volume pulse rise velocities triggered PVEs at a lower instantaneous pulse amplitude than lower rise velocities, further corroborating the dependence of stretch-activated arrhythmias on the velocity of stretch. In contrast, an increase in the basic ventricular volume had no effect on the probability of PVE occurrence during the volume pulses. The MAP recordings demonstrated spatial variability in the extent of local depolarizations and site of PVE origin; transient depolarizations occurred, and PVEs originated most often in the posterolateral region of the left ventricle. CONCLUSIONS. Membrane depolarization is caused by both gradual and rapid ventricular stretch, but PVEs are more easily elicited by rapid stretch. Regions of greater myocardial compliance that experience greater relative stretch may act as "foci" for stretch-activated arrhythmias during dynamic ventricular loading. These whole-heart data corroborate the existence of stretch-activated membrane channels in ventricular myocardium and may help explain ventricular ectopy under conditions of differential ventricular loading, as in ventricular dyskinesia, or regional muscle traction, as in mitral valve prolapse syndrome.

[Effect of tetradrine on electrophysilogic changes caused by rising of left ventricular preload in guinea pigs]

XX Wang — 2006-06-09T08:44:43-00:00

Zhongguo Zhong Yao Za Zhi, Vol. 28, No. 11. (November 2003), pp. 1054-1056.

OBJECTIVE: To investigate the changes of guinea pig heart electrophysiological properties caused by increasing left ventricular preload, and to assess the effects of tetradrine on these changes. METHOD: Working model preparation of guinea pig hearts in vitro was used, and the preload of left ventricle was increased by adjusting the prefusion pressure of left atria. The changes of heart electrophysiologic parameters including monophasic action potential duration (MAPD90), monophasic action potential amplitude (MAPA), effective refractory period (ERP) and ventricular fibrillation threshold (VFT) were observed before and after altering the preload of left ventricle, and compared in the absence and presence of tetradrine, streptomycin or verapamil. RESULT: The rising of left ventricular preload led to shortening of MAPD90, ERP, and to descent of MAPA, VFT (all P<0.01). Both Tetradrine and streptomycin inhibited these changes of heart electrophysiologic parameters caused by elevation of left ventricular afterload (all P<0.01). In contrast, verapamil had no effects on the preload-related electrophysiological changes (all P>0.05). CONCLUSION: Electrophysiologic changes caused by increasing left ventricular preload may be inhibited by tetrandrine, through inhibition of stretch-activated ion channels.

A rat genetic linkage map and comparative maps for mouse or human homologous rat genes

J Yamada — 2007-03-29T20:10:15-00:00

Mammalian Genome, Vol. 5, No. 2. (1 February 1994), pp. 63-83.

Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry.

Gert Jan Boender — 2007-04-25T10:53:54-00:00

PLoS Comput Biol, Vol. 3, No. 4. (20 April 2007)

Devastating epidemics of highly contagious animal diseases such as avian influenza, classical swine fever, and foot-and-mouth disease underline the need for improved understanding of the factors promoting the spread of these pathogens. Here the authors present a spatial analysis of the between-farm transmission of a highly pathogenic H7N7 avian influenza virus that caused a large epidemic in The Netherlands in 2003. The authors developed a method to estimate key parameters determining the spread of highly transmissible animal diseases between farms based on outbreak data. The method allows for the identification of high-risk areas for propagating spread in an epidemiologically underpinned manner. A central concept is the transmission kernel, which determines the probability of pathogen transmission from infected to uninfected farms as a function of interfarm distance. The authors show how an estimate of the transmission kernel naturally provides estimates of the critical farm density and local reproduction numbers, which allows one to evaluate the effectiveness of control strategies. For avian influenza, the analyses show that there are two poultry-dense areas in The Netherlands where epidemic spread is possible, and in which local control measures are unlikely to be able to halt an unfolding epidemic. In these regions an epidemic can only be brought to an end by the depletion of susceptible farms by infection or massive culling. The analyses provide an estimate of the spatial range over which highly pathogenic avian influenza viruses spread between farms, and emphasize that control measures aimed at controlling such outbreaks need to take into account the local density of farms.

Maximum A Posteriori Speckle Filtering And First Order Texture Models In Sar Images

A Lopes — 2005-11-11T15:45:33-00:00

Geoscience and Remote Sensing Symposium, 1990. IGARSS '90. 'Remote Sensing Science for the Nineties'., 10th Annual International (1990), pp. 2409-2412.

Steerable wedge filters for local orientation analysis

EP Simoncelli — 2005-09-30T07:43:55-00:00

Image Processing, IEEE Transactions on, Vol. 5, No. 9. (1996), pp. 1377-1382.

Steerable filters have been used to analyze local orientation patterns in imagery. Such filters are typically based on directional derivatives, whose symmetry produces orientation responses that are periodic with period π, independent of image structure. We present a more general set of steerable filters that alleviate this problem

Adaptive restoration of images with speckle

D Kuan — 2005-11-08T10:46:43-00:00

Acoustics, Speech, and Signal Processing [see also IEEE Transactions on Signal Processing], IEEE Transactions on, Vol. 35, No. 3. (1987), pp. 373-383.

Speckle is a granular noise that inherently exists in all types of coherent imaging systems. The presence of speckle in an image reduces the resolution of the image and the detectability of the target. Many speckle reduction algorithms assume speckle noise is multiplicative. We instead model the speckle according to the exact physical process of coherent image formation. Thus, the model includes signal-dependent effects and accurately represents the higher order statistical properties of speckle that are important to the restoration procedure. Various adaptive restoration filters for intensity speckle images are derived based on different model assumptions and a nonstationary image model. These filters respond adaptively to the signal-dependent speckle noise and the nonstationary statistics of the original image.

A refined gamma MAP SAR speckle filter with improved geometrical adaptivity

A Baraldi — 2005-11-11T18:03:42-00:00

Geoscience and Remote Sensing, IEEE Transactions on, Vol. 33, No. 5. (1995), pp. 1245-1257.

A modified version of the refined gamma maximum-a-posteriori (RGMAP) speckle filter, which is found in the literature, is presented. The traditional RGMAP speckle filter first defects contours belonging to step edges and thin linear structures, then applies the RGMAP filter to local statistics extracted from rectangular masks that do not cross image contours. The proposed modified RGMAP (MRGMAP) filter first exploits local operators belonging to the odd-symmetric filter category employed by RGMAP to detect image segments, then it computes local statistics over areas that are not necessarily rectangular, but are subsets of the image segments having any possible shape. Therefore, MRGMAP enhances the RGMAP ability in exploiting shape adaptive windowing near image contours, where speckle is not fully developed. The MRGMAP computation time is estimated to be of the same magnitude of that of the original RGMAP, the latter depending on the number of filter categories being employed. The qualitative and quantitative results of the MRGMAP filter applied to real SAR images are satisfactory as the filter seems to be effective in speckle removal whereas it retains edge sharpness and subtle details. However, tests on simulated SAR images must still be performed in order to provide definitive evidence supporting MRGMAP effectiveness. Since MRGMAP typically removes image structures featuring a constant reflectivity gradient, this filter is not particularly suitable for image enhancement in human photo-interpretation. MRGMAP can be rather employed as a preprocessing module in a computer-based SAR image classification procedure based on segment mean value analysis

Maps of the brain.

AW Toga — 2005-10-31T15:27:47-00:00

Anat Rec, Vol. 265, No. 2. (April 2001), pp. 37-53.

We review recent developments in brain mapping and computational anatomy that have greatly expanded our ability to analyze brain structure and function. The enormous diversity of brain maps and imaging methods has spurred the development of population-based digital brain atlases. These atlases store information on how the brain varies across age and gender, across time, in health and disease, and in large human populations. We describe how brain atlases, and the computational tools that align new datasets with them, facilitate comparison of brain data across experiments, laboratories, and from different imaging devices. The major methods are presented for the construction of probabilistic atlases, which store information on anatomic and functional variability in a population. Algorithms are reviewed that create composite brain maps and atlases based on multiple subjects. We show that group patterns of cortical organization, asymmetry, and disease-specific trends can be resolved that may not be apparent in individual brain maps. Finally, we describe the creation of four-dimensional (4D) maps that store information on the dynamics of brain change in development and disease. Digital atlases that correlate these maps show considerable promise in identifying general patterns of structural and functional variation in human populations, and how these features depend on demographic, genetic, cognitive, and clinical parameters.

Silhouette maps for improved texture magnification

Pradeep Sen — 2005-12-21T09:02:06-00:00

(2004), pp. 65-73.

Colour photometric stereo: simultaneous reconstruction of local gradient and colour of rough textured surfaces

S Barsky — 2008-01-15T11:00:27-00:00

Computer Vision, 2001. ICCV 2001. Proceedings. Eighth IEEE International Conference on, Vol. 2 (2001), pp. 600-605 vol.2.

Classification of a rough 3D surface from 2D images may be difficult due to directional effects introduced by illumination. One possible way of dealing with the problem is to extract the local albedo and gradient surface information which do not depend on the illumination, and classify the texture directly using these intrinsic characteristics. In this paper we present an algorithm for simultaneous recovery of local gradient and colour using multiple photometric images. The algorithm is proven to be optimal in the least squares error sense. Experimental results with real images and comparison with other approaches are also presented

Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses

John Bowers — 2008-04-25T03:18:36-00:00

Proceedings of the National Academy of Sciences, Vol. 102, No. 37. (13 September 2005), pp. 13206-13211.

Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible "euchromatin" and "heterochromatin." Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond. 10.1073/pnas.0502365102

Functional Lateralization of Face, Hand, and Trunk Representation in Anatomically Defined Human Somatosensory Areas

SB Eickhoff — 2008-06-17T19:00:25-00:00

Cereb. Cortex (27 March 2008), bhn039.

We used functional magnetic resonance imaging (fMRI) and cytoarchitectonic probability maps to investigate the responsiveness of individual areas in the human primary and secondary somatosensory cortices to hand, face, or trunk stimulation of either body-side. A Bayesian modeling approach to quantify the probability of ipsilateral activations revealed that areas OP 1, OP 4, and OP 3 of the SII cortex as well as the trunk and face representations within all SI subareas (areas 3b, 1, and 2) show robust bilateral responses to unilateral stimulation. Such bilateral response properties are in good agreement with the transcallosal projections demonstrated for these areas in nonhuman primates and other mammals. In contrast, the SI hand region showed a different pattern. Whereas ipsilateral areas 3b and 1 were deactivated by tactile hand stimulation, particularly on the left, there was strong evidence for ipsilateral processing of information from the right hand in area 2. These results demonstrate not only the behavioral importance of the hand representation, but also suggest that area 2 may have particularly evolved to form the cortical substrate of these specialized demands, in line with recent studies on cortical evolution hypothesizing that area 2 has developed with increasing manual abilities in anthropoid primates featuring opposable thumbs. 10.1093/cercor/bhn039

Intraoperative Intrinsic Optical Imaging of Neuronal Activity from Subdivisions of the Human Primary Somatosensory Cortex

Katsushige Sato — 2008-06-17T23:42:21-00:00

Cereb. Cortex, Vol. 12, No. 3. (1 March 2002), pp. 269-280.

We performed intrinsic optical imaging of neuronal activity induced by peripheral stimulation from the human primary somatosensory cortex during brain tumor surgery for 11 patients. After craniotomy and dura reflection, the cortical surface was illuminated with a xenon light through an operating microscope. The reflected light passed through a bandpass filter, and we acquired functional images using an intrinsic optical imaging system. Electrical stimulation of the median nerve, or the first and fifth digits, induced biphasic intrinsic optical signals which consisted of a decrease in light reflectance followed by an increase. The decrease in light reflectance was imaged, and we identified a neural response area within the crown of the postcentral gyrus. In experiments on first and fifth digit stimulation, we identified optical responses in separated areas within the crown of the postcentral gyrus, i.e. near the central sulcus and near the postcentral sulcus. In the former response area, separate representations of the two fingers were observed, whereas in the latter response area, the two fingers were represented in the same region. A similar somatotopic representation was observed with electrical stimulation of the first and third branches of the trigeminal nerve. These results seem to support the hypothesis of hierarchical organization in the human primary somatosensory cortex. 10.1093/cercor/12.3.269

Mobile Mapping and Geographic Information Systems

Keith Clarke — 2004-11-26T01:21:49-00:00

Cartography and Geographic Information Science, Vol. 31, No. 3. (1 July 2004), pp. 131-136.

Mobile mapping and geographic information systems may represent a new paradigm for cartography and GIScience. This short foreword to the special issue introduces the three papers that follow, briefly surveys the growing literature of field and mobile GIS, and discusses the emerging literature surrounding wearable GIS and their augmented reality display systems. The UCGIS research agenda for mobile and distributed computing is presented, as are the calls for additional research in the papers of the special issue. Calls for a comprehensive review article of the field from a cartography/GIScience perspective, and for involvement in the research agenda of mobile systems, are made.

A somatotopic map of vibrissa motion direction within a barrel column

Mark Andermann — 2006-03-27T16:11:32-00:00

Nature Neuroscience, Vol. 9, No. 4. (19 March 2006), pp. 543-551.

Suboptimal tradeoffs in information seeking

Wai-Tat Fu — 2005-12-16T19:33:26-00:00

Cognitive Psychology, Vol. In Press, Corrected Proof

Explicit information-seeking actions are needed to evaluate alternative actions in problem-solving tasks. Information-seeking costs are often traded off against the utility of information. We present three experiments that show how subjects adapt to the cost and information structures of environments in a map-navigation task. We found that subjects often stabilize at suboptimal levels of performance. A Bayesian satisficing model (BSM) is proposed and implemented in the ACT-R architecture to predict information-seeking behavior. The BSM uses a local decision rule and a global Bayesian learning mechanism to decide when to stop seeking information. The model matched the human data well, suggesting that adaptation to cost and information structures can be achieved by a simple local decision rule. The local decision rule, however, often limits exploration of the environment and leads to suboptimal performance. We propose that suboptimal performance is an emergent property of the dynamic interactions between cognition and the environment.

A Gene Expression Map of the Arabidopsis Root

Kenneth Birnbaum — 2007-03-30T13:20:29-00:00

Science, Vol. 302, No. 5652. (12 December 2003), pp. 1956-1960.

A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of more than 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics. 10.1126/science.1090022

Computer aided interpretation of lexical cooccurrences

Paola Velardi — 2005-10-20T22:32:21-00:00

(1989), pp. 185-192.

Under the hood of GeoVRML 1.0

Martin Reddy — 2005-11-10T13:38:50-00:00

(2000), pp. 23-28.

Map Algebra Extended with Functors for Temporal Data

Andrew Frank — 2007-02-13T03:11:46-00:00

: Perspectives in Conceptual Modeling (2005), pp. 194-207.

Neuronal selectivity and local map structure in visual cortex.

I Nauhaus — 2008-03-24T14:20:27-00:00

Neuron, Vol. 57, No. 5. (13 March 2008), pp. 673-679.

The organization of primary visual cortex (V1) into functional maps makes individual cells operate in a variety of contexts. For instance, some neurons lie in regions of fairly homogeneous orientation preference (iso-orientation domains), while others lie in regions with a variety of preferences (e.g., pinwheel centers). We asked whether this diversity in local map structure correlates with the degree of selectivity of spike responses. We used a combination of imaging and electrophysiology to reveal that neurons in regions of homogeneous orientation preference have much sharper tuning. Moreover, in both monkeys and cats, a common principle links the structure of the orientation map, on the spatial scale of dendritic integration, to the degree of selectivity of individual cells. We conclude that neural computation is not invariant across the cortical surface. This finding must factor into future theories of receptive field wiring and map development.

Inferring causal relationships among different histone modifications and gene expression

Hong Yu — 2008-06-19T04:53:55-00:00

Genome Res. (18 June 2008), gr.073080.107.

Histone modifications are major epigenetic factors regulating gene expression. They play important roles in maintaining stem cell pluripotency and in cancer pathogenesis. Different modifications may combine to form complex "histone codes." Recent high throughput technologies, such as "ChIP-chip" and "ChIP-seq," have generated high resolution maps for many histone modifications on the human genome. Here we use these maps to build a Bayesian network to infer causal and combinatorial relationships among histone modifications and gene expression. A pilot network derived by the same method among polycomb group (PcG) genes and H3K27 trimethylation is accurately supported by current literature. Our unbiased network model among histone modifications is also well supported by cross validation results. It not only confirmed already known relationships, such as those of H3K27me3 to gene silencing, H3K4me3 to gene activation, and the effect of bivalent modification of both H3K4me3 and H3K27me3, but also identified many other relationships that may predict new epigenetic interactions important in epigenetic gene regulation. Our automated inference method, which is potentially applicable to other ChIP-chip or ChIP-seq data analyses, provides a much-needed guide to deciphering the complex histone codes. 10.1101/gr.073080.107

Discovery of knowledge flow in science

Hai Zhuge — 2006-05-08T15:25:26-00:00

Commun. ACM, Vol. 49, No. 5. (May 2006), pp. 101-107.

Participatory GIS a people's GIS?

Christine Dunn — 2007-11-04T23:40:36-00:00

Prog Hum Geogr, Vol. 31, No. 5. (1 October 2007), pp. 616-637.

Recent years have witnessed a burgeoning of applications of GIS which grant legitimacy to indigenous geographical knowledge as well as to `official' spatial data. By incorporating various forms of community participation these newer framings of Geographical Information Systems as `Participatory GIS' (PGIS) offer a response to the critiques of GIS which were prevalent in the 1990s. This paper reviews PGIS in the context of the `democratization of GIS'. It explores aspects of the control and ownership of geographical information, representations of local and indigenous knowledge, scale and scaling up, web-based approaches and some potential future technical and academic directions. 10.1177/0309132507081493

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.

TH Kim — 2007-07-24T10:04:56-00:00

Cell, Vol. 128, No. 6. (23 March 2007), pp. 1231-1245.

Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites.

A high-resolution map of active promoters in the human genome

Tae Kim — 2005-07-01T19:24:29-00:00

Nature (29 June 2005)

Neural correlates of human wayfinding in stroke patients.

M van Asselen — 2006-07-02T03:26:41-00:00

Brain Res, Vol. 1067, No. 1. (5 January 2006), pp. 229-238.

Wayfinding is a complex cognitive function involving different types of information, such as knowledge about landmarks and direction information. This variety of processes suggest that multiple neural mechanisms are involved, e.g., the hippocampal system, the posterior parietal and temporal cortical areas. Although patient studies and imaging studies have given important insights in the exact neural circuitry underlying wayfinding, many controversies remain. Therefore, the current study sets out to further examine the neuroanatomical correlates of wayfinding in a sample of 31 stroke patients with unilateral lesions, tested with a series of different wayfinding tasks, including landmark recognition, landmark ordering, route reversal and route drawing. For all patients, the exact location of their lesion was determined using CT or MRI scans. Based on existing literature, a number of relevant brain areas were demarcated, after which the extent of damage to these areas was determined for each patient separately. Performance on the landmark recognition task was impaired by damage to the right hippocampal formation, whereas a weak correlation was found between damage to the dorsolateral prefrontal cortex and processing the order of the landmarks. Several brain areas were found to be involved in retracing a route from the end to the beginning, including the right hippocampal formation, the right posterior parietal cortex, the right dorsolateral prefrontal cortex and the right temporal lobe. Finally, damage to the right temporal lobe impaired the ability to draw the route.

Cartography and Science in Early Modern Europe: Mapping the Construction of Knowledge Spaces

David Turnbull — 2008-01-29T12:23:31-00:00

Science and cartography have had an intimate history which has not been simply the creation of ever more accurate scientific maps but one in which science, cartography and the state have co-produced the knowledge space that provides the conditions for the possibility of modern science and cartography. The central cartographic process is the assemblage of local knowledges and, as such, is a particular form of the assembly processes fundamental to science. The first attempts by the state to create a space within which to assemble cartographic knowledge were at the Casa da Mina and the Casa de la Contratación, and hence they can be described as the first scientific institutions in Europe. Their failure to create a knowledge space can be attributed to the nature of the portolan charts. The triangulation of France and the linking of the Greenwich and Paris Observatories established the kind of knowledge space that now constitutes the dominant form within which modern science and cartography are produced. However, resistance to the hegemony of modern scientific knowledge space remains possible through finding alternative ways of assembling local knowledge. / Science et cartographie sont intimement liées dans leur histoire, qui ne consiste pas à dresser des cartes toujours plus exactes, mais dans laquelle science, cartographie et État ont créé l'espace de connaissance qui a fourni les conditions nécessaires à la science et à la cartographie modernes. L'essence du développement cartographique réside dans la réunion de la connaissance des lieux, et ainsi est un aspect particulier des développements fondamentaux pour la science. On trouve réunies très tôt des tentatives par l'État de créer un espace épistémologique pour la connaissance cartographique dans la péninsule ibérique, où la Casa da Mina et la Casa de Contratación peuvent se targuer d'être les plus anciennes institutions scientifiques des débuts de l'Europe moderne. Ces tentatives échouèrent du fait que les cartes-portulans avaient leurs propres traditions de navigation, indépendamment de l'État. Un exemple tardif est la triangulation de la France et la liaison des Observatoires de Greenwich et de Paris, qui créa l'espace de connaissance de la science et de la cartographie modernes. Cependant on peut aussi trouver d'autres façons de réunir la connaissance des lieux et les espaces de création de la connaissance. / Wissenschaft und Kartographie hatten eine innige Geschichte, nicht eine von immer genaueren Karten, sondern eine in welcher Wissenschaft, Kartographie und Staat den Kenntnisraum schufen um die Voraussetzungen für eine moderne Wissenschaft und Kartographie zu liefern. Der zentrale kartographische Prozeß ist eine Ansammlung von örtlicher Kenntnis. Es ist eine besondere Form des Prozeßes, fundamental gegenüber jeder Wissenschaft. Frühe Beispiele von Bemühungen durch den Staat um einen erkenntnistheoretischen Raum zu schaffen, in welchem kartographische Kenntnis zusammengetragen werden konnte, waren auf der Iberischen Halbinsel, wo die Casa da Mina und die Casa de la Contratación sich berufen können die ersten wissenschaftliche Institute des frühen modernen Europas zu sein. Diese Bemühungen mißlungen da die Portolankarten ihre eigenen, vom Staat unabhängigen, Navigationstraditionen hatten. Ein späteres Beispiel ist die Triangulation von Frankreich, und die Zusammenarbeit der Observatorien in Greenwich und Paris, welche den Kenntnisraum der modernen Wissenschaft und Kartographie gründeten. Auch alternative Wege der Zusammenstellung von lokaler Kenntnis und der Schaffung von Kenntnisräumen können ebenfalls gefunden werden.

Led (astray) by genetic maps: the cartography of the human genome and health care.

A Lippman — 2008-04-30T08:33:17-00:00

Social science & medicine (1982), Vol. 35, No. 12. (December 1992), pp. 1469-1476.

Advocates of projects to map the human genome claim that the information produced will illuminate the causes of human disease, improve treatment and, in general, increase our health and well-being. While concerns about the costs of mapping and the possible discriminatory and eugenic applications of the information it will provide have received some attention, assumptions implicit in the biomedical discourse in which its 'benefits' are proposed and which are shaping definitions of illness and health, normality and abnormality, have not yet been adequately analyzed. This paper examines how the genetic stories about mapping and its potential products being told in the biomedical (and popular) literature continue a tradition of reductionism and determinism. This new 'cartography', by adopting the blueprint as a metaphor for genes, leads to restricted conceptions of health and illness, reinforces inequities in the distribution of health and, by privatizing and individualizing responsibility for health, creates and legitimizes a new arena for social control.

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.

B Schoeberl — 2005-08-23T11:51:39-00:00

Nat Biotechnol, Vol. 20, No. 4. (April 2002), pp. 370-375.

We present a computational model that offers an integrated quantitative, dynamic, and topological representation of intracellular signal networks, based on known components of epidermal growth factor (EGF) receptor signal pathways. The model provides insight into signal-response relationships between the binding of EGF to its receptor at the cell surface and the activation of downstream proteins in the signaling cascade. It shows that EGF-induced responses are remarkably stable over a 100-fold range of ligand concentration and that the critical parameter in determining signal efficacy is the initial velocity of receptor activation. The predictions of the model agree well with experimental analysis of the effect of EGF on two downstream responses, phosphorylation of ERK-1/2 and expression of the target gene, c-fos.

Revealing targeted therapy for human cancer by gene module maps.

DJ Wong — 2008-06-18T09:24:05-00:00

Cancer research, Vol. 68, No. 2. (15 January 2008), pp. 369-378.

A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of cancers should be treated is unknown. Here, we show that a gene module map can guide the prospective identification of targeted therapies for genetic subtypes of cancer. By visualizing genome-scale gene expression in cancer as combinations of activated and deactivated functional modules, gene module maps can reveal specific functional pathways associated with each subtype that might be susceptible to targeted therapies. We show that in human breast cancers, activation of a poor-prognosis "wound signature" is strongly associated with induction of both a mitochondria gene module and a proteasome gene module. We found that 3-bromopyruvic acid, which inhibits glycolysis, selectively killed breast cells expressing the mitochondria and wound signatures. In addition, inhibition of proteasome activity by bortezomib, a drug approved for human use in multiple myeloma, abrogated wound signature expression and selectively killed breast cells expressing the wound signature. Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies.

Module map of stem cell genes guides creation of epithelial cancer stem cells.

DJ Wong — 2008-06-18T09:18:20-00:00

Cell stem cell, Vol. 2, No. 4. (10 April 2008), pp. 333-344.

Self-renewal is a hallmark of stem cells and cancer, but existence of a shared stemness program remains controversial. Here, we construct a gene module map to systematically relate transcriptional programs in embryonic stem cells (ESCs), adult tissue stem cells, and human cancers. This map reveals two predominant gene modules that distinguish ESCs and adult tissue stem cells. The ESC-like transcriptional program is activated in diverse human epithelial cancers and strongly predicts metastasis and death. c-Myc, but not other oncogenes, is sufficient to reactivate the ESC-like program in normal and cancer cells. In primary human keratinocytes transformed by Ras and I kappa B alpha, c-Myc increases the fraction of tumor-initiating cells by 150-fold, enabling tumor formation and serial propagation with as few as 500 cells. c-Myc-enhanced tumor initiation is cell-autonomous and independent of genomic instability. Thus, activation of an ESC-like transcriptional program in differentiated adult cells may induce pathologic self-renewal characteristic of cancer stem cells.

Various methods for the mapping of science

L Leydesdorff — 2006-12-07T06:54:02-00:00

Scientometrics, Vol. V11, No. 5. (26 May 1987), pp. 295-324.

Identifying a better measure of relatedness for mapping science

Richard Klavans — 2006-12-18T06:18:39-00:00

Journal of the American Society for Information Science and Technology, Vol. 57, No. 2. (2006), pp. 251-263.

Measuring the relatedness between bibliometric units (journals, documents, authors, or words) is a central task in bibliometric analysis. Relatedness measures are used for many different tasks, among them the generating of maps, or visual pictures, showing the relationship between all items from these data. Despite the importance of these tasks, there has been little written on how to quantitatively evaluate the accuracy of relatedness measures or the resulting maps. The authors propose a new framework for assessing the performance of relatedness measures and visualization algorithms that contains four factors: accuracy, coverage, scalability, and robustness. This method was applied to 10 measures of journal-journal relatedness to determine the best measure. The 10 relatedness measures were then used as inputs to a visualization algorithm to create an additional 10 measures of journal-journal relatedness based on the distances between pairs of journals in two-dimensional space. This second step determines robustness (i.e., which measure remains best after dimension reduction). Results show that, for low coverage (under 50%), the Pearson correlation is the most accurate raw relatedness measure. However, the best overall measure, both at high coverage, and after dimension reduction, is the cosine index or a modified cosine index. Results also showed that the visualization algorithm increased local accuracy for most measures. Possible reasons for this counterintuitive finding are discussed.

Computer-aided clustering of citation networks as a tool of mapping of research trends in biomedicine

YK Duplenko — 2006-12-18T07:07:19-00:00

Scientometrics, Vol. V32, No. 3. (26 March 1995), pp. 247-258.

Quadratic programming relaxations for metric labeling and Markov random field MAP estimation

Pradeep Ravikumar — 2007-03-12T10:24:57-00:00

(2006), pp. 737-744.

Reconstructing dynamic regulatory maps.

J Ernst — 2007-01-19T09:21:39-00:00

Mol Syst Biol, Vol. 3 (2007)

Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein-DNA interactions that allows the specific regulation of genes needed for the response. We have developed a novel computational method that uses an input-output hidden Markov model to model these regulatory networks while taking into account their dynamic nature. Our method works by identifying bifurcation points, places in the time series where the expression of a subset of genes diverges from the rest of the genes. These points are annotated with the transcription factors regulating these transitions resulting in a unified temporal map. Applying our method to study yeast response to stress, we derive dynamic models that are able to recover many of the known aspects of these responses. Predictions made by our method have been experimentally validated leading to new roles for Ino4 and Gcn4 in controlling yeast response to stress. The temporal cascade of factors reveals common pathways and highlights differences between master and secondary factors in the utilization of network motifs and in condition-specific regulation.

Map-based navigation in mobile robots:: I. A review of localization strategies

David Filliat — 2007-01-23T12:37:37-00:00

Cognitive Systems Research, Vol. 4, No. 4. (December 2003), pp. 243-282.

For a robot, an animal, and even for man, to be able to use an internal representation of the spatial layout of its environment to position itself is a very complex task, which raises numerous issues of perception, categorization and motor control that must all be solved in an integrated manner to promote survival. This point is illustrated here, within the framework of a review of localization strategies in mobile robots. The allothetic and idiothetic sensors that may be used by these robots to build internal representations of their environment, and the maps in which these representations may be instantiated, are first described. Then map-based navigation systems are categorized according to a three-level hierarchy of localization strategies, which respectively call upon direct position inference, single-hypothesis tracking, and multiple-hypothesis tracking. The advantages and drawbacks of these strategies, notably with respect to the limitations of the sensors on which they rely, are discussed throughout the text.

Yeast two-hybrid contributions to interactome mapping

Jodi Parrish — 2006-08-08T09:50:22-00:00

Current Opinion in Biotechnology, Vol. 17, No. 4. (August 2006), pp. 387-393.

Interactome mapping, the systematic identification of protein interactions within an organism, promises to facilitate systems-level studies of biological processes. Using in vitro technologies that measure specific protein interactions, static maps are being generated that include many of the protein networks that occur in vivo. Most of the binary protein interaction data currently available was generated by large-scale yeast two-hybrid screens. Recent efforts to map interactions in model organisms and in humans illustrate the promise and some of the limitations of the two-hybrid approach. Although these maps are incomplete and include false positives, they are proving useful as a framework around which to elaborate and model the in vivo interactome.

How to make large self-organizing maps for nonvectorial data

Teuvo Kohonen — 2008-01-30T02:59:20-00:00

Neural Networks, Vol. 15, No. 8-9. ( 2002), pp. 945-952.

The self-organizing map (SOM) represents an open set of input samples by a topologically organized, finite set of models. In this paper, a new version of the SOM is used for the clustering, organization, and visualization of a large database of symbol sequences (viz. protein sequences). This method combines two principles: the batch computing version of the SOM, and computation of the generalized median of symbol strings.

Nucleosome organization in the Drosophila genome.

Travis N Mavrich — 2008-04-16T22:48:07-00:00

Nature (13 April 2008)

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

Self-organizing hierarchic networks for pattern recognition in protein sequence

J Hanke — 2007-10-10T22:10:04-00:00

Protein Sci, Vol. 5, No. 1. (1 January 1996), pp. 72-82.